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The effect of neighbor species' phylogenetic and trait difference on tree growth in subtropical forests

To comprehensively understand ecological dynamics within a forest ecosystem, it is vital to explore how surrounding trees influence the growth of individual trees in a community. Biotic interactions have a significant potential impacts on individual tree growth and their effects can be evaluated through trait and phylogenetic-based approaches. This study investigates the relative importance of biotic interactions on tree growth by examining several metrics and considering three classes of intrinsic growth rates among the focal individuals: slower, intermediate and faster-growing trees. The metrics include hierarchical and absolute trait differences of focal trees to neighbors, neighborhood crowding index, phylogenetic distance, and trait community metrics. Our results indicated that the phylogenetic distance between the focal tree and its neighbors positively impacted the growth of all classes, whereas different traits have distinct effects on slower and faster-growing trees. Specific leaf area (SLA) and leaf area (LA) showed hierarchical importance to tree growth. Trees surrounded by neighbors with higher SLA and LA than themselves grow better, particularly for slower-growing trees. Higher levels of wood density difference between the focal trees and their neighbors positively impacts slower and faster-growing trees, while height difference negatively impacts faster-growing trees. We conclude that the interactions between trees are mediated by their ecological differences, but the performance and responses to surrounding competitors vary along with their growth class within a community. This study has revealed that the tree's intrinsic growth rate mediates the effect of traits and phylogeny of surrounding trees on individual tree growth.

Diet-induced plasticity of life-history traits and gene expression in outbred Drosophila melanogaster population

Food is fundamental for the survival of organisms, governing growth, maintenance, and reproduction through the provision of essential macronutrients. However, access to food with optimum macronutrient composition, which will maximize the evolutionary fitness of an organism, is not always guaranteed. This leads to dietary mismatches with potential impacts on organismal performance. To understand the consequences of such dietary mismatches, we examined the effects of isocaloric diets varying in macronutrient composition on eight key organismal traits spanning across the lifespan of a large outbred Drosophila melanogaster population (n ~ 2500). Our findings reveal that carbohydrate-reduced isocaloric diets correlates to accelerated pre-adult development and boosts reproductive output without impacting pre-adult viability and body size. Conversely, an elevated dietary carbohydrate content correlated to reduced lifespan in flies, evidenced by accelerated functional senescence including compromised locomotor activity and deteriorating gut integrity. Furthermore, transcriptomic analysis indicated a substantial difference in gene regulatory landscapes between flies subject to high carbohydrate vs high protein diet, with elevated protein levels indicating transcriptomes primed for reduced synthesis of fatty acids. Taken together, our study helps advance our understanding of the effect of macronutrient composition on life history traits and their interrelations, offering critical insights into potential adaptive strategies that organisms might adopt against the continual dietary imbalances prevalent in the rapidly evolving environment.

Phenotypic traits of 17 populations of Spartina alterniflora in China

Understanding the ecological and evolutionary processes that underlie phenotypic and genetic variation among invasive plant populations and the capacity of such populations to colonize a broad range of environments is a major goal in ecology. Rapid adaptation to local environmental conditions often leads to latitudinal clines in both phenotypes and genotypes of invasive plant species. Previous studies suggest that natural selection influenced a latitudinal cline in phenotypic traits of the invasive plant Spartina alterniflora in China. However, little is understood of the relationship between genetic and phenotypic differentiation and environmental factors among S. alterniflora populations. Here, we studied whether S. alterniflora exhibits a latitudinal cline in genetic diversity across the east coast of China and whether genetic and phenotypic differentiation among populations were correlated with environmental factors. The Restriction-site Associated DNA (RAD-seq) sequencing was used to obtained genomic information of 17 populations of S. alterniflora in China. A redundancy analysis (RDA) was performed to assess whether environmental variables were corelated with genetic and phenotypic differentiation among the populations. A univariate environmental association analysis (implemented through Latent Factor Mixed Model; LFMM) and a principal component analysis (PCAdapt) were used to test for signature of local adaptation. A total of 3, 310 SNPs showed a clear genetic structure among populations in three climatic regions (northern, mid-latitude and southern). Positive correlations between genetic differentiation and variation in reproductive characteristics of S. alterniflora were revealed, suggesting that sexual reproduction traits might be stable and genetically heritable. Outlier loci that were identified by both PCAdapt and LFMM methods were significantly correlated to soil phosphorus content, soil salinity, and precipitation. These results provide evidence of molecular signatures of local adaptation of S. alterniflora and suggest that rapid adaptive evolution may facilitate invasiveness of S. alterniflora in China.

Data for: Fire season and time since fire determine AM fungal trait responses to fire management

Rationale: AM fungi are common mutualists in grassland and savanna systems that are adapted to recurrent fire disturbance. This long-term adaptation to fire means that AM fungi display disturbance associated traits which are useful for understanding environmental and temporal effects on AM fungal community assembly. Methods: In this work, we evaluated how fire driven ecological selection on AM fungal spore traits varies with fire season (Fall vs. Spring) and time since fire. We tested this by analyzing AM fungal spore traits (e.g., colorimetric, sporulation, and size) from a fire regime experiment. Key results: Immediately following Fall and Spring fires, spore pigmentation darkened; however, this did not mediate the observed differences between Fall burned and no burn communities. Six months after Fall fires, spores in burned plots were lower in volume, produced less color rich pigment, and had higher sporulation rates, and these differences in spore traits were associated with shifts in AM fungal spore communities. Main conclusion: This shows that AM fungal responses to fire vary based on season (stronger effects in the Fall) and with time since fire. Variation in AM fungal responses to fire time may reflect greater exposure to fire in Fall, when sporulation is highest.

Fifteen physiological traits related to osmoregulation and reactive oxygen species metabolism in two life form aquatic plants under a natural water salinity gradient on the Tibetan Plateau and Northwest China

Aquatic plants, as the primary producers, determine the community structure and ecological function of freshwater ecosystems. However, salinization threatens inland freshwater wetlands and thus the survival of aquatic plants. Exploring the plant physiological responses to increasing water salinity could enhance our understandings of plant adaptive strategies under future climate change regimes in wetlands. We measured 15 physiological traits of 49 aquatic plant species along a large environmental gradient in alpine and arid regions of western China, to explore the physiological adaptions and compare the similarities and differences in adaptive strategies between the two life forms to natural water salinity. We found that both water salinity and low temperature were key factors affecting aquatic plants in alpine and arid regions. Aquatic plants adapt to saline habitats by accumulating proline and sulfur (S) concentrations, and to cold habitats by increasing ascorbate peroxidase activity. Plant trait network analysis showed that the hub trait in emergent plants was S, but in submerged plants was proline, suggesting that emergent plants balanced osmoregulation and reactive oxygen metabolism via S-containing compounds, while submerged plants prioritizing the regulation of osmotic balance via proline.

opencc-zeroDec 2023View details →

Stem decomposition of temperate tree species is determined by stem traits and fungal community composition during early stem decay

Dead trees are vital structural elements in forests playing key roles in the carbon and nutrient cycle. Stem traits and fungal community composition are both important drivers of stem decay, and thereby affect ecosystem functioning, but their relative importance for stem decomposition over time remains unclear. To address this issue, we used a common garden decomposition experiment in a Dutch larch forest hosting fresh logs from 13 common temperate tree species. In total 25 fresh wood and bark traits were measured as indicators of wood accessibility for decomposers, nutritional quality, and chemical or physical defense mechanisms. After one and four years of decay, we assessed the richness and composition of wood-inhabiting fungi using amplicon sequencing and determined the proportional wood density loss. Average proportional wood density loss for the first year was 18.5%, with further decomposition occurring at a rate of 4.3% yr-1 for the subsequent three years across tree species. Proportional wood density loss varied widely across tree species in the first year (8.7-24.8% yr-1) and subsequent years (0-11.3% yr-1). The variation was directly driven by initial wood traits during the first decay year, then later directly driven by bark traits and fungal community composition. Moreover, bark traits affected the composition of wood-inhabiting fungi and thereby indirectly affected decomposition rates. Specifically, traits promoting resource acquisition of the living tree, such as wide conduits that increase accessibility and high nutrient concentration, increased initial wood decomposition rates. Fungal community composition, but not fungal richness explained differences in wood decomposition after four years of exposure in the field, where fungal communities dominated by brown-rot and white-rot Basidiomycetes were linked to higher wood decomposition rate. Synthesis. Understanding what drives deadwood decomposition through time is important to understand the dynamics of carbon stocks. Here, using a tailor-made experimental design in a temperate forest setting, we have shown that stem trait variation is key to understanding the roles of these drivers; Initially, wood traits explained decomposition rates while subsequently, bark traits and fungal decomposer composition drove decomposition rates. These findings inform forest management with a view to selecting tree species to promote carbon storage.

Data from: Relationships between rhizosphere microbial communities, soil abiotic properties and root trait variation within a pine species

Rhizosphere microbes play important roles in plant performance and ecosystem functioning. It is becoming increasingly clear that rhizosphere communities vary with soil properties and variation in root traits among plant species. However, less is known about whether and how variation in root traits within plant species influences the rhizosphere microbial communities. We evaluated the intraspecific root traits variation and explored their associations with bacterial and fungal communities in rhizosphere by focusing on an ectomycorrhizal tree species, i.e., Pinus massoniana, in 22 sites in subtropical China. The first dimension of the principal component analysis on root traits revealed evidence for the 'conservation' gradient of the root economics space. Overall, root traits explained more variation in fungal communities than in bacterial communities in the rhizosphere. Functional composition of rhizosphere microbial communities changed significantly along the 'conservation' gradient, with fast-growing copiotrophic bacteria and symbiotic ectomycorrhizal fungi were significantly enriched on the 'acquisition' side, while slow-growing oligotrophic bacteria were significantly enriched on the 'conservation' side of the gradient. Synthesis: Our study demonstrates that intraspecific variation in plant roots significantly influence rhizosphere microbial communities, which in turn can influence plant nutrition and therefore plant performance within the community.

opencc-by-4.0Mar 2024View details →

Minimal dataset for the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".

Dataset "lin2024-sex_combined_interaction-association_signifincant_in_one_or_more_tests-summary.txt" is a minimal dataset to reproduce the figures and tables in the manuscript "Better together against genetic heterogeneity: a sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank".  To generate this dataset, see "https://github.com/BoxiLin/t2meta" Steps 0, 1. This dataset is the input for Steps 2, 3, 4, 5 to generate Figures 1-3 and Table 2-3.   ##### Column information ######################## The following columns are annotations on each variant in the GWAS, calculated across the analysis subset of 361,194 samples by the Neale lab: code: Phenotype identifier in the form of "[UKB Data field]_raw" variant: Unique variant identifier in the form "chr:pos:ref:alt", where "ref" is aligned to the forward strand. chr: Chromosome of the variant. pos: Position of the variant in GRCh37 coordinates. rsid: rs ID ref: Reference allele on the forward strand. alt: Alternate allele (not necessarily minor allele). p_hwe: Hardy-Weinberg p-value. info: Imputation INFO score as provided by UK Biobank.   The following columns are sex-stratified test statistics calculated by the Neale lab: minor_allele.x: Minor allele (AF < 0.5) in the female GWAS  minor_AF.x: Minor allele frequency in the female GWAS  beta.x: Estimated effect size of alt allele in the female GWAS  se.x: Estimated standard error of beta in the female GWAS tstat.x: t-statistic of beta estimate (= beta/se) in the female GWAS  pval.x: p-value of beta significance test in the female GWAS  minor_allele.y: Minor allele (AF < 0.5) in the male GWAS  minor_AF.y: Minor allele frequency in the male GWAS  beta.y: Estimated effect size of alt allele in the male GWAS  se.y: Estimated standard error of beta in the male GWAS  tstat.y: t-statistic of beta estimate (= beta/se) in the male GWAS  pval.y: p-value of beta significance test in the male GWAS    The following columns are sex-combined test statistics calculated in our analysis: T.I: test statsitic for interaction effect-only  p.T.I:  p-value of the interaction effect-only test  TSG.L:  test statsitic for inverse variance weighted meta-analysis p.TSG.L: p-value of the inverse variance weighted meta-analysis TSG.Q: test statsitic for the omnibus meta-analysis p.TSG.Q: p-value for the omnibus meta-analysis

opencc-by-4.0Mar 2024View details →

Trait values of European tetrapods archetypes

This dataset contains trait values used to identify archetype groups among European tetrapods. The file includes 8 data sheets, one for each homogeneous group of tetrapods and one sheet about references.

opencc-by-4.0Dec 2021View details →

Tropical forest seedling trait data collected in Danum Valley, Sabah, Malaysia, in February 2020

Data Link This is a link to a dataset affiliated with SEARRP but that is stored in a different repository. Please find the link to the dataset below, and be sure to cite the data correctly via that repository. Correct Citation Burslem, D.F.R.P.; Banin, L.F.; Bartholomew, D.C.; Bin Suis, M.A.F.; Bittencourt, P.R.L.; Chapman, D.; Dent, D.H.; Hayward, R.M.; O’Brien, M.J.; Rowland, L.M. (2022). Tropical forest seedling trait data collected in Danum Valley, Sabah, Malaysia, in February 2020. (Dataset). NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/e738e8af-554a-4940-bb56-267c7377d74d Summary This dataset includes values of 15 traits (total dry mass; root length to shoot length ratio; leaf mass fraction; root mass fraction; shoot mass fraction; leaf thickness; leaf force to punch; leaf area to shoot area ratio; leaf concentrations of N, P, K, Ca and Mg; leaf N: P concentration ratio; specific maximum root length) measured in February 2020 on 394 seedlings of 15 woody plant species growing in logged in the Ulu Segama Forest Reserve or unlogged forest in the Danum Valley Conservation Area, Malaysia. The purpose of this data collection was to determine whether the expression of plant functional traits differed between tree seedlings recruited into logged and unlogged forests. This information is important for understanding the drivers of variation in seedling growth and survival in response to logging disturbance, and to uncover the mechanisms giving rise to differentiation in tree seedling composition in response to logging. These data were collected as part of NERC project “Seeing the fruit for the trees in Borneo: responding to an unpredictable community-level fruiting event” (NE/T006560/1). Link to project website: <a href="https://gtr.ukri.org/projects?ref=NE%2FT006560%2F1" target="_blank" rel="noopener">https://gtr.ukri.org/projects?ref=NE%2FT006560%2F1</a> Link to data repository: <a href="https://doi.org/10.5285/e738e8af-554a-4940-bb56-267c7377d74d" target="_blank" rel="noopener">https://doi.org/10.5285/e738e8af-554a-4940-bb56-267c7377d74d</a>

Data and code from: Similar trait-based successional assembly in native and introduced plants despite species pool differences

What drives the composition of invaded communities and the local abundance of introduced species are key questions in ecology. Community-assembly theory provides a useful framework for addressing these questions. Specifically, the environmental filtering model of community assembly predicts that a species' presence and abundance in a community depends on the interaction between its functional traits and the local environmental filters. However, for introduced species, larger-scale dispersal and introduction-related filters may restrict their regional trait pool. Here we tested this framework using long-term data from 50+ years of old-field vegetation succession. We asked whether native and introduced plant assemblages followed the same trait-based assembly rules. We also asked whether local functional dissimilarities between the two can be explained by regional species pool differences, a possibility that has rarely been addressed. We found strong similarities in the assembly processes of native and introduced plants. Average height and seed mass of both groups increased over time, consistent with previous studies of old-field succession. Moreover, the two showed similar trait-abundance relationships. While there were also some differences, particularly in their trait-incidence relationships, these differences appeared to be minor.Further, we identified species pool constraints on introduced species, and found that the exotic species pool was biased towards early successional traits. Lastly, we found that highly invasive exotic species were also likely to deviate from the expected trait-abundance relationship, suggesting a link between the two. These results suggest that introduced species generally follow the same assembly rules as native species. They also indicate that species pool differences can result in local functional composition differences, even when the two groups follow the same assembly rules. Moreover, there may be a link between species invasiveness and deviation from assembly rules, which, if further confirmed, provides a potential method of identifying strong invaders.

Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population

Body size variation is central in the evolution of life history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a Genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis. The putatively associated variants explained 12.8% to 44.5% of the total phenotypic variation in body size and were mapped to genes with functional roles in the regulation of gene expression and cell cycle processes. Our study is the first to provide insights into the genetic basis of complex traits in newts and provides a useful tool to identify loci potentially involved in fitness related traits in small data sets from natural populations in non-model species.

opencc-by-4.0Mar 2024View details →

EMMA-X GWAS results on S. pimpinellifolium RSA traits - part 3

The results of GWAS run through EMMA-X pipeline, on root system architecture traits of S. pimpinellifolim (wild tomato) exposed to control and salt stress conditions on agar plates. Traits are abbreviated as: LRnG for increase in lateral root number, LRno for lateral root number, MR.GR for main root growth rate, MRL for main root length. The treatments are abbreviated with C or S for control or 100 mM NaCl treatments. The numbers in file name (0-4) indicate the days post transfer to agar plates containing treatment.

The dissection of a despotic society: exploration, dominance and hormonal traits

Naked mole-rats (Heterocephalus glaber) live in large colonies with one breeding female (queen), one to three breeding males, and the remainder are non-reproductive subordinates. We investigated how the dominance ranking position in naked mole-rats differs with exploration (the propensity to explore a novel environment), and endocrine related markers. Faecal progestagen metabolite (fPM), glucocorticoid metabolite (fGCM), androgen metabolite (fAM) metabolite, and plasma prolactin concentrations were quantified in breeding, high, middle and low ranked females and males. There were no significant differences between the dominance ranking positions and exploration behaviour. Interestingly, the queens and high-ranking females had higher fGCM and fAM concentrations compared to middle and low ranked females; possibly due to an increased possibility of conflict with each other. The queen had significantly higher fPM concentrations than all other ranked females since she is responsible for procreation. In the males, the breeding males had higher fGCM concentrations compared to high and low ranked males. However, breeding males and middle-ranking males had overall higher prolactin levels than all other ranked males and these individuals may indirectly contribute to greater cooperative care and burrow maintenance. We suggest that high-ranking females exhibit higher fGCM and fAM concentrations possibly due to competition with the queen.

opencc-by-4.0Apr 2024View details →

Forest inventory, leaf area index, and leaf functional traits of various land cover classes in Kulen, Cambodia

<ol><li>Sub-title 1: Forest inventory of evergreen forest, regrowth forest, and evergreen forest in Kulen, Cambodia. (File name: Forest_Inventory_Pub.txt)  </li><li>Sub-title 2: Species leaf area, chlorophyll a and b and leaf dry matter content of 30 species collected from evergreen forests, regrowth forests, and cashew plantation in Kulen, Cambodia. (File name: Leaf_Trait_Species_Pub.txt)</li><li>Sub-title 3: Canopy and total leaf area index from evergreen forests, regrowth forests, and cashew plantation in Kulen, Cambodia. (File name: LAI_Pub.txt )</li></ol>

opencc-by-4.0Apr 2024View details →

Phylogenetic trees and morphological traits dataset of Geonoma palm genus

The phylogenetic trees correspond to the Geonoma genus and Geonomateae tribe phylogenies based on a concatenation analysis of 20 small informative genes and the csv file corresponds to the mean value of 24 morphological traits for 68 Geonoma species based on Henderson (2012) dataset.

opencc-zeroApr 2024View details →

Below-ground root nutrient-acquisition strategies are more sensitive to long-term grazing than above-ground leaf traits across a soil nutrient gradient

Understanding how plant nutrient acquisition strategies respond to grazing at the community level is critical to understanding ecosystem structure and functioning in grasslands. However, few studies have simultaneously compared the difference in aboveground (leaf) and belowground (root) nutrient-acquisition strategies in response to long-term grazing, especially at the regional scale. Here, we measured a set of leaf and fine-root traits that correspond to the fast-slow economic spectrum at the community level in 10 experimental sites from paired grazed and ungrazed grasslands across a soil nutrient gradient covering three major types of grasslands in northern China. We found that patterns of variations of leaf and fine-root traits were consistent with both a leaf and root economic spectrum at the community level for both grazed and non-grazed plots. Grazing had a minor effect on community-level leaf nutrient-acquisition strategies but strongly influenced community-level root nutrient-acquisition strategies. Specifically, root nutrient-acquisition strategies were shifted to more exploitative resource use in grazed communities. Moreover, soil nutrients contributed to the changes in both leaf and root nutrient-acquisition strategies, which tended towards a more resource-acquisition strategy with increasing soil nutrient levels. Grazing significantly interacted with soil nutrients to affect root nutrient-acquisition strategies, and grazing contributed more to root nutrient-acquisition strategies than soil nutrients. Our results demonstrated completely inconsistent responses of community-level above- and below-ground resource acquisition strategies to long-term grazing, and below-ground acquisition strategies were more sensitive to long-term grazing. Our findings also suggest that high-intensity anthropogenic activities such as grazing may strongly modify below-ground resource acquisition strategies.

opencc-by-4.0Apr 2024View details →

Leveraging interindividual variability in threat conditioning of inbred mice to model trait anxiety

Abstact Trait anxiety is a major risk factor for stress-induced and anxiety disorders in humans. However, animal models accounting for the inter-individual variability in stress vulnerability are largely lacking. Moreover, the pervasive bias of using mostly male animals in preclinical studies poorly reflects the increased prevalence of psychiatric disorders in women. Using the threat imminence continuum theory, we designed and validated an auditory aversive conditioning-based pipeline in both female and male mice. We operationalized trait anxiety by harnessing the naturally occurring variability of defensive freezing responses combined with a model-based clustering strategy. While sustained freezing during prolonged retrieval sessions was identified as an anxiety-endophenotype biomarker in both sexes, females were consistently associated with an increased freezing response. RNA-sequencing of CeA, BLA, ACC and BNST revealed massive differences in phasic and sustained responders’ transcriptomes, correlating with transcriptomic signatures of psychiatric disorders, particularly PTSD. Moreover, we detected significant alterations in the excitation/inhibition balance of principal neurons in the lateral amygdala. These findings provide compelling evidence that trait anxiety in inbred mice can be leveraged to develop translationally relevant preclinical models to investigate mechanisms of stress susceptibility in a sex-specific manner. Remarks This submission contains the analysis code and source data to fully reproduce the behavioural, electrophysiology and RNA-seq analysis described in Kovlyagina et al.   - Navigate to the behaviour_ephys directory and run the scripts to reproduce the behavioural and electrophysiology analysis - Navigate to the RNAseq directory and run the script to reproduce the RNA-seq analysis

opencc-zeroApr 2024View details →

Vertical stratification of leaf physical traits exerts bottom-up pressures on insect herbivory in a sugar maple temperate forest

Do vertical gradients in temperate forest structure insect herbivore communities? We tested the hypothesis that the increase in light intensity from understory to forest canopy level drives differences in leaf physical traits and budburst phenology that impact insect herbivores and thus play a role in structuring both herbivore communities and the leaf damages they cause. Twelve sugar maple (Acer saccharum) sites were monitored in southern Quebec, examining insect herbivore patterns from understory to the shaded and sun canopy over the summers of 2020, 2021, and 2022. Additionally, we recorded leaf physical traits, temperature, humidity, and sun exposure. Our findings revealed that leaf thickness increased along the vertical gradient in 2021, making leaves less favorable to herbivores in the canopy level. Accordingly, we recorded a consistent decrease in insect herbivory damage rates from the understory to the shaded canopy and sun canopy in 2020 and 2021, driven by leaf cutters, skeletonizers, stipplers, and leaf miners. These results support our hypothesis that variation in plant physical traits due to sun exposure contributes to the vertical stratification of insect damage. In 2022, the gradient of insect herbivore abundance corroborated the observed damage trends from the previous years. Moreover, we calculated an average annual herbivory rate of 9.1% of the leaf surface in our study site, suggesting limited evidence supporting a significant contribution of background herbivory to the decline of sugar maple forests. Overall, our study highlights the importance of vertical gradients in structuring insect herbivore communities and emphasizes the role of leaf traits in mediating these interactions.